VDJbase: an adaptive immune receptor genotype and haplotype database
Open Access
- 11 October 2019
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 48 (D1), D1051-D1056
- https://doi.org/10.1093/nar/gkz872
Abstract
VDJbase is a publicly available database that offers easy searching of data describing the complete sets of gene sequences (genotypes and haplotypes) inferred from adaptive immune receptor repertoire sequencing datasets. VDJbase is designed to act as a resource that will allow the scientific community to explore the genetic variability of the immunoglobulin (Ig) and T cell receptor (TR) gene loci. It can also assist in the investigation of Ig- and TR-related genetic predispositions to diseases. Our database includes web-based query and online tools to assist in visualization and analysis of the genotype and haplotype data. It enables users to detect those alleles and genes that are significantly over-represented in a particular population, in terms of genotype, haplotype and gene expression. The database website can be freely accessed at https://www.vdjbase.org/, and no login is required. The data and code use creative common licenses and are freely downloadable from https://bitbucket.org/account/user/yaarilab/projects/GPHP.Funding Information
- Horizon 2020 (825821)
- ISF (832/16)
- NIH (1R01AI127877, 1R01AI125567, 1R01AI130398)
This publication has 35 references indexed in Scilit:
- A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing dataBioinformatics, 2018
- Differences in Allelic Frequency and CDRH3 Region Limit the Engagement of HIV Env Immunogens by Putative VRC01 Neutralizing Antibody PrecursorsCell Reports, 2016
- Ageing of the B-cell repertoirePhilosophical Transactions B, 2015
- Single B-cell deconvolution of peanut-specific antibody responses in allergic patientsJournal of Allergy and Clinical Immunology, 2015
- Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing dataBioinformatics, 2015
- Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing.Integrative Biology, 2015
- The promise and challenge of high-throughput sequencing of the antibody repertoireNature Biotechnology, 2014
- Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number VariationAmerican Journal of Human Genetics, 2013
- B-cell–lineage immunogen design in vaccine development with HIV-1 as a case studyNature Biotechnology, 2012
- IMGT(R), the international ImMunoGeneTics information system(R)Nucleic Acids Research, 2008